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182 results • Page
2 of 4
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3
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1
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609
views
Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 8 months ago by
Ram
43k • written 8 months ago by
Juke34
8.5k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 8 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
1
vote
0
replies
658
views
Tutorial:
How to convert gene ids in R
computational-biology
gene-id
rstats
updated 8 months ago by
Ram
43k • written 8 months ago by
Ming Tommy Tang
★ 3.9k
19
votes
13
replies
9.8k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 4 months ago by
jude
• 0 • written 21 months ago by
ATpoint
81k
2
votes
0
replies
3.1k
views
Tutorial:
How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix
Seurat
single-cell
rstats
updated 8 months ago by
Ram
43k • written 8 months ago by
Ming Tommy Tang
★ 3.9k
19
votes
7
replies
6.4k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 8 months ago by
ATpoint
81k • written 4.0 years ago by
colindaven
6.3k
4
votes
2
replies
1.0k
views
Tutorial:
How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC
transcription
factor
ChIP-seq
8 months ago by
Ming Tommy Tang
★ 3.9k
93
votes
23
replies
90k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 10 weeks ago by
clara.apicella
• 0 • written 5.7 years ago by
otwtgin2010
▴ 610
2
votes
0
replies
449
views
Tutorial:
Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering
gene-expression
rstats
updated 8 months ago by
Ram
43k • written 8 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
0
replies
732
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
9 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
625
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
622
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling
R
Computational-Biology
9 months ago by
sinha.shriprakash
▴ 20
1
vote
2
replies
847
views
Tutorial:
How to ask computational biology questions
computational-biology
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
668
views
Tutorial:
How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix
scRNA-seq
single-cell
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
0
replies
706
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
9 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
589
views
Tutorial:
How to make a perfect heatmap using RNAseq data
heatmap
RNAseq
rstats
9 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
648
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
9 months ago by
Coremine Medical
▴ 20
2
votes
0
replies
683
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 9 months ago by
Ram
43k • written 9 months ago by
Coremine Medical
▴ 20
4
votes
0
replies
924
views
Tutorial:
How to make a heatmap in R and deep understand it
heatmap
r
10 months ago by
Ming Tommy Tang
★ 3.9k
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 10 months ago by
GenoMax
140k • written 10.4 years ago by
Obi Griffith
20k
1
vote
0
replies
796
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 4 months ago by
Ram
43k • written 12 months ago by
Milad
▴ 10
3
votes
2
replies
2.6k
views
Tutorial:
Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences
Workshops
updated 10 months ago by
Ram
43k • written 6.9 years ago by
jnowacki
▴ 100
7
votes
3
replies
2.4k
views
Tutorial:
Automated dbSNP lookup by rsID position, plus genome build liftover
rsid
hg19
liftover
hg38
dbsnp
updated 11 months ago by
Randy H
▴ 110 • written 19 months ago by
Kevin Blighe
87k
2
votes
0
replies
1.1k
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 4 months ago by
Ali
• 0 • written 14 months ago by
firestar
★ 1.6k
7
votes
2
replies
2.4k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
8 months ago by
Dr.Animo
▴ 110
2
votes
0
replies
1.2k
views
Tutorial:
GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo
R
data-mining
Gene-pathway-enrichment
RNA-Seq
updated 9 months ago by
Ram
43k • written 15 months ago by
Novogene
▴ 410
1
vote
0
replies
2.5k
views
Tutorial:
GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo
R
data-mining
differential-gene-expression
RNA-Seq
updated 9 months ago by
Ram
43k • written 15 months ago by
Novogene
▴ 410
5
votes
0
replies
1.5k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 9 months ago by
Ram
43k • written 15 months ago by
Novogene
▴ 410
1
vote
2
replies
1.5k
views
Tutorial:
ViennaRNA package installation in Windows
windows
rna
mfold
viennarna
updated 9 months ago by
Ram
43k • written 18 months ago by
Sandhiya
▴ 20
11
votes
7
replies
11k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 10 months ago by
Ram
43k • written 3.1 years ago by
Novogene
▴ 410
83
votes
34
replies
18k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 10 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 9 months ago by
Ram
43k • written 5.1 years ago by
jaybee
▴ 170
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 7 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
3
votes
1
reply
3.3k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
updated 7 weeks ago by
MaxF
▴ 120 • written 2.7 years ago by
Kevin Blighe
87k
239
votes
176
replies
94k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 10 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
6
votes
2
replies
4.9k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
3 months ago by
GenoMax
140k
21
votes
26
replies
9.4k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 14 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
73
votes
27
replies
27k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by
snardeli
• 0 • written 10.1 years ago by
Istvan Albert
100k
65
votes
15
replies
14k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 10 months ago by
Ram
43k • written 5.5 years ago by
finswimmer
16k
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.4 years ago by
elia.brodsky
▴ 340
22
votes
2
replies
6.0k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 11 months ago by
Ram
43k • written 7.4 years ago by
Eric Lim
★ 2.1k
0
votes
0
replies
1.2k
views
Tutorial:
In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence
cloud
dna
sequencing
updated 10 months ago by
Ram
43k • written 5.7 years ago by
corlinp
• 0
20
votes
2
replies
8.0k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 10 months ago by
Ram
43k • written 6.4 years ago by
bernatgel
★ 3.4k
2
votes
0
replies
1.4k
views
Tutorial:
Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq
next-gen
updated 10 months ago by
Ram
43k • written 5.8 years ago by
elia.brodsky
▴ 340
1
vote
4
replies
3.3k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
3
votes
4
replies
4.4k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 10 months ago by
Ram
43k • written 5.9 years ago by
chen
★ 2.5k
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 10 months ago by
Ram
43k • written 6.9 years ago by
Sej Modha
5.3k
2
votes
0
replies
1.5k
views
Tutorial:
Webinar: Extracting research evidence from publications
text-mining
ontology
pubmed
updated 10 months ago by
Ram
43k • written 6.1 years ago by
Maria_Levchenko
▴ 60
0
votes
0
replies
3.6k
views
Tutorial:
SFA (Stochastic Frontier Analysis) STATA 14
R
updated 10 months ago by
Ram
43k • written 6.1 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
1.6k
views
Tutorial:
PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 10 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
182 results • Page
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Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Mapping ortholog human and mouse transcript
by
1769mkc
★ 1.2k
for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
by
Mensur Dlakic
★ 26k
Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
Answer: Tissue specific mRNA expression dataset in human and mouse
by
BioinfGuru
★ 1.6k
Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
Answer: Mapping ortholog human and mouse transcript
by
BioinfGuru
★ 1.6k
That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
Comment: How do I get the gene annotations as a text file from a genebank file?
by
BioinfGuru
★ 1.6k
Can you upload or post a link to the genbank file please?
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
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